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Intro Puzzles
Here you can see the original instructions of the intro puzzles. Translations: Deutsch | Svenska Tip : read carefully the texts, press on button "tell me more", reset the puzzle after a few try and redo. Sidechains Level 1-1: One Small Clash This is a protein. We need your help to fold it into the right shape! You can drag SIDECHAINS with the mouse. Get rid of the clash by clicking and dragging one of the sidechains away from the other. Level 1-2: Swing It Around Swing It Around 1.png Swing It Around 2.png You can't see the sidechains from this angle! Click and drag on the white background to''' rotate the view'. You can also move or zoom by holding ctrl or shift while you drag. Watch your score! It tells you how well the protein is folded. '''Level 1-3 : Shake' You've earned the SHAKE tool! You can use shake to fix clashes for you! When you think SHAKE has done a good enough job, you can press it again to Stop. Old version Level 1-4: Shake It Off Orange together, blue apart. You can zoom in and out. Hold shift and drag the background. The backbone is red with clashes! Make it green. You've earned a new tool! SHAKE mo.ves all the sidechains at once. It will find a good spot for each of them. Stop the Shake by pressing the space bar Backbone packing Level 2-1: When Backbones Collide This is the BACKBONE of the protein. Sometimes the backbone is too close together. Click and drag the backbone to pull it appart! You can always Undo. Shake will adjust the sidechains for you." Level 2-2: Close the Gap Ot her times the backbone is too far apart. VOIDS are an indicator that there is empty space that needs to be filled. Try getting rid of some of the voids by dragging the backbone together! Remember to use SHAKE to get rid of the clashes! Oops, the helices are too far apart. Want to reset?" Level 2-3: Wiggle You now have access to a VERY powerful tool: the WIGGLE tool! Just like SHAKE tries to take care of sidechains, WIGGLE tries to let Foldit improve the backbone. WIGGLE gets stuck if it cannot increase the score. Click this button again to stop the tool. old version Level 2-3: Twin Pack The curly helices are too far apart! Pack the helices closely, so the hydrophobics are squished between them. Then Shake and Wiggle! You can pack this protein tighter by bringing the HELICES together. VOIDS (red balls) are empty spaces in the protein. You can compact the protein to pop them Shake will get rid of clashes. Wiggle works best without clashes. Wiggle takes care of the tiny adjustments that are too small to make by pulling. Oops, the helices are too far apart. Want to reset? Even if your score went down, try a Shake then Wiggle combination to get more points! tip : move an helix closer to the other, Shake and wiggle Level 2-4: Triple Packed The hydrophobics in the center are exposed! Bury as many hydrophobics as you can. Orange sidechains want to be surrounded. Sometimes it is a better strategy to restrict your move to certain segments.You can choose such segments by selecting them. Click on a segment to select it. Selected segments will turn blue. You can stop this helix from moving. Middle click or hold shift and click it to FREEZE.You can Freeze parts of the protein to hold them in place while you pull. Just hold shift and double click the area you want to Freeze. Shake will get rid of clashes. Don't worry about individual sidechains. Shake should be enough for this puzzle. You can pull this helix in closer. Those voids need to be popped! Shake and Wiggle when you're close. Wiggle tries out small backbone movements. It gets stuck if none of them increase the score. As many have problems with this one, here is LennStar's guide, proofed to be working several times: If you have done anythink, restart the puzzle. (best from puzzle menu if you have rotated the view) '' Now, as the puzzle is fresh, do it this way: Take the lonely upper helix at the point where the arrow from the hint is pointing. Now move the mouse down-left to the red balls. (the voids, if you don't see them, either activate them in the views options, or target the one red hydrophobic in the foreground) If a clash appears, pull a little bit more and stop. Now shake and wiggle. That should do the trick. Congratulations! Hydrogen Bonding '''Level 3-1: Sheets Together' Its ti me to learn about the best things for improving your score in Foldit - Hydrogen bonds! Try pressing Wiggle. Those blue and white bands are Hydrogen Bonds. They form when these zig-zaggy sheets line up together like this. Level 3-2: Lonely Sheets Time to matc h up some sheets! Wiggle doesn't always work by itself. You can connect these sheets with RUBBER BANDS. Hold shift and drag from one to the other. Try it with this sheet! Hold shift and drag. Rubber Bands pull together when you Wiggle. Don't worry about individual sidechains. Try connecting the sheets with a Rubber Band. tip : put rubber bands between to two little sheets, wiggle, remove bands, shake and wiggle Level 3-3: Sheets and Ladders Thre e sheets have been torn apart! Rubber Bands are free! Make as many as you want. You can move the view around and drag the background. When you're close, you can remove the bands and Wiggle again. tip : put a rubber band at each end of the sheet with the end of the sheet above, wiggle, remove the bands, shake and wiggle. The step ladder are the sheets and the side the bands Le Foldit 1297974789.png Foldit 1297974837.png vel 3-4: Lock and Lower One of the sheets is out of place! Sheets like to be alongside each other. Remember, hydrogen bonds are great for your score. You can Freeze the sheets already in place. Hold shift and double click. tip ; one sheet is over the row, freeze the 2 sheets on each side of it, double click on them, put the sheet between this two, rotate to see if the protein is flat, shake and wiggle, Level 3-5: rebuild You might have guessed by now, but''' color''' is used to show how well part of the protein is folded. This loop appears to be a problem. You can deal with problematic segments by using the REBUILD '''tool. Rebuild tests out different shapes for the protein. Right click (for windows) on the backbone to start a Rebuild. You can stop when Rebuild finds the shape you want. Shake and Wiggle will take care of clashes. This looks like a good shape! Try a Shake and Wiggle to clean it up. You can Wiggle a single section. Right click and choose Wiggle Hydrophobics and Hydrophilics '''Level 1-3: Hide the Hydrophobic http://images.wikia.com/foldit/images/9/96/Hide.pngAdded by MsuchardThe big hydrophobic sidechain is out in the open! Orange sidechains are HYDROPHOBIC. They want to be buried inside the protein. EXPOSEDS may appear on unburied hydrophobics! (yellow ball moving) Blue sidechains need plenty of space. They should point outward. Orange sidechains should be kept surrounded. Hide it in the empty space in the protein's interior and move the blue hydrophilic away outside. Your score measures not only clashes, but also how well hydrophobics are hidden. tip : move the orange sidechain in the center. Sequences Level 4-1: Basic Threading This level will intriduce the powerful Alignment tool. It will let you use the structure of real proteins, called TEMPLATES, by THREADING. Click on the smiley button to bring up the ALIGNMENT tool. This 3D strcutures shows the backbone of the template. (ball and sticks) The bottom row of the letters is the TEMPLATE SEQUENCE. you can see it in 3D as spheres connected by lines. The top row of letters is the sequance of your protein. The cylinders in 3D show how its backbones lines up with the template. When you THREAD, your protein will try to fit onto the 3D template where the cylinders are. Click the little smiley to try threading. Now that you've threaded it, try a shake and wiggle! Level 4-2: Alignin' Sequences'This time the letters and colors in the sequences are not lined up well! This middle row shows how well each letter matches; a bigger white bar means a better match and this score ''(at the end of the line) ''shows how the sequences match overall. You can click and drag or use the arrow keys to move the letters around. Try to line up the colors. It's okay if there are spaces, but fewer spaces is better. Click here (''little smiley) to thread when they match well!. Threading didn't work. Try to find a better match. Letters that blink red after trying to thread are causing problems. With a good alignment, you'll just need to use the ALIGNMENT tool to thread, then wiggle and shake. '''Level 4-3: A major shift The sequences don't always line up perfectly. You can look at the template structure to get an idea of what threading will do. A space in your sequence will stretch your protein when it is threaded. A space in the template sequence will squash your protein when it is threaded. Use the sequences to line this purple part up and make a good sheet; watch how the 3D structure moves when you change the aligment. But be careful how you align this loop! Look at the structure and keep any stretched segments away from the rest of the protein. Threading didn't work. Put the only space after this letter! Letters that blink red after trying to thread are causing problems. Focus on this loop, and try to reduce any stretching, but keep a good alignment! tips : see the image, wait for the thread a long time, shake a long time and wiggle Level 4-4: Rebuild Repairs The red loop is stuck in the wrong shape! Try using the Rebuild tool to open up that loop. You'll see it when you ctrl click on the loop. You've started to Rebuild the backbone! The protein will try out some different shapes. Once it looks good enough, click Stop Rebuild and try a Shake and Wiggle to get rid of clashes. Tweak and Rebuild Level 5-1: Turn It Down The helix has turned and exposed a hydrophobic! Rotate it back into place with the Tweak tool. You'll see it when you ctrl click on the helix. You've started a Tweak! Click and hold on the purple arrows to rotate the protein in the direction you want it to go. Watch your score! If you turn it too far, you can try turning it back or just Undo. Level 5-2: The Right Rotation Find the one helix that needs rotating and fix it with the Tweak tool! Look for a hydrophobic sticking out in the open, and turn it back in. You can always Undo. The sidechains disappear when at the right place. Level 5-3: Flippin' Sheets One of the sheets is twisted the wrong way! Look for the sheet with the exposed hydrophobics, and click the new straight arrows on the Tweak tool to shift and flip it. You've started a Tweak! Click and hold on the curved purple arrows to rotate the protein in the direction you want it to go or use the straight purple arrows to shift and flip the sheet in that direction. Watch your score! If you turn it too far, you can try turning it back or just Undo. LennStar's guide: This is one puzzle that really dislikes being mishandled. It took me at least 5 tries. This is how to do it: If you already have done anything to it, reset the puzzle. (Hint: You propably have to move the 4 sheets to the foreground, the one with the arrow pointing on with the short end to the left. You can also go back to puzzle menu to get the right view.) Now right click on the one sheet where the arrow from the text points to. Click tweak. Now click one time on the straight arrow to the right. Now the sheet should flip. use shake and wiggle it. That should raise your score to the needed points. Level 5-4: Rubber Band Reversal A hydrophobic is flipped the wrong way! Reverse the zig zag with two Rubber Bands and a Rebuild: one band to bring the hydrophobic down, and another to bring the hydrophilic up. You can attach a Rubber Band to empty space! Level 5-5: Moving along Sometimes you can move whole piece of the protein.Click on a piece to bring on up the move tool. Then press and hold down RIGHT BUTTON anaywhere on the tool to drag the piece around. Tip : Click on the helix, then on the purple star with the right button, then move the helix on the shadow, rotate the view to check then shake and wiggle. Protein Design Level 6-1: Intro to Design Learn to change the side chains using the Design Mode tool. Level 6-2: Swapping Side Chains Change some more sidechains using the Design Mode tool. Level 6-3: Mass Mutate Change some sidechains by hand using the Design Mode tool. When you have change enough sidechains, you will be introduced to the Mutate command. Level 6-4: Insertion and Deletion ''' In Design Mode you can right click on the backbone and change the length of the backbone. More molecules '''Level 7-3: DNA Pairing Use Design Mode to find the correct match for the incorrectly paired sidechains. DNA sidechains pair according to color and size. Match sidechains of same color and opposite sizes to make lots of bonds! Level 7-4: DNA and Protein DNA can hydrogen bond to protein. Mutate the proteins to form better bonds.